RetrogeneDB ID:

retro_amel_440

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192442.1:889564..890709(-)
Located in intron of:ENSAMEG00000009387
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSAMEG00000018411
Aliases:None
Description:Importin subunit alpha [Source:UniProtKB/TrEMBL;Acc:D2HQA5]


Retrocopy-Parental alignment summary:






>retro_amel_440
CAGCAGTGCAGTTCCCCCACTGCCAACCTTACAGATTCAAGAACAGGGGAAAGACAGTATAAAAATGAGGTGGTGCCGAG
TTGAAGTTAATGTGGACCTGAGGAAAGCTTAGAAGGAAGACTAGATGCTGAAAAGGAGAAATGTAAGCTCATTTCTTGAT
AATGCTACTTCTCCACTGCGGGAAAACCCGCAACAACCAGGGGAGTGTACGTTGGTCTGTTGATAACATTGTCAAAGGCA
TAAGTAGCAATAATTTGGGAAGCCACCTCCAGGCTACTCAAGCTGCTAAGAAACTGCTTTCTGTGGAAAAGCAGCCTACG
TAGACAACATAATCTGGGCTGGTTTGATTCCGGCATTTGTGTTCTTTTTGGACAGAAATGTTCATAGTCCCATTCAATTG
AATCTGTTTGAGCCCTCACTAACATTGCTTCTTGGATATCAGAACAGACCGAGGCTGTGGTAGATAGAGATGCTATCCCA
GCATTCATTTCTCCATTGACATCTTCCCATGCTCACATCAGTGAACAAGTTGTATGAGGTCTAGGAAACATTACACAAAA
TAGTTCAGTATTCTGAGACTTGGTTATCAAATATAGTGCATTTGACCCACTGTTGGTCCTTCTTGCAGTTCCTGATATAT
CATCTTTAGCATGTGGTTACTTAGATAATCTTACCTGGACACTTTCAAATTTTTGTTCCGGCAAGGATCATACACTCACG
TAGGTGCTATTGAGGAAATTCTTCCCACTTTAGTTCATCTGCATTGCAGTGATCCAGAAGTATTAGGAGATACCTGCTGG
ATCATTACTTACCATACTGTTGGTCCAAATGAACAGATTGAAATGGTTGTGAAAAGAGGAGTTGTGCCCCAGTTTGTGAA
ACTTTGGAGAGAGCTCCTGAATTGCTAATTGTGACTTCTGTGTTAAGAGCTATAGGAAGTATTGTCACTGGGACAGACGA
ACAGACTCAAGTTGTAATAGATGTGGGAGCATTTGCCATCTTTCCCAGCCTGTAATGACCCCCAAAACTAATACTCAGAA
GGAAGCAATGTGGAAATGTAAAACATGACATCTGCCTGCCAGGACCAGACACAGTAAGTTGTGAATCAAGGATTAGTCCC
ATTTCTCATTGGCATTCTAAGGAAG

ORF - retro_amel_440 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.01 %
Parental protein coverage: 72.59 %
Number of stop codons detected: 8
Number of frameshifts detected 10


Retrocopy - Parental Gene Alignment:

ParentalENANSPAARLN-RFKNKGK-DSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQEN-RNNQ
....SP.A.L..RFKN.GK.DS..MR..R.EVNV.LRKA.K.D.MLKRRNVSSF.D.ATSPL.EN.RNNQ
RetrocopyQQCSSPTANLT<RFKNRGK<DSIKMRWCRVEVNVDLRKA*KED*MLKRRNVSSFLDNATSPLREN>RNNQ
ParentalGTVNWSVDDIVKGINSNNLESQLQATQAARKLLSREKQPP-IDNIIRAGLIPKFVSFLGRTDCSPIQF-E
G.V.WSVD.IVKGI.SNNL.S.LQATQAA.KLLS.EKQP...DNII.AGLIP.FV.FL.R...SPIQ..E
RetrocopyGSVRWSVDNIVKGISSNNLGSHLQATQAAKKLLSVEKQPT<VDNIIWAGLIPAFVFFLDRNVHSPIQL<E
ParentalSAWALTNIASGTSEQTKAVVDGGAIPAFISLLASSHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPL
S..ALTNIAS..SEQT.AVVD..AIPAFIS.L.SSHAHISEQ.V..LGNI....SVF.DLVIKY.A.DPL
RetrocopySV*ALTNIASWISEQTEAVVDRDAIPAFISPLTSSHAHISEQVV*GLGNITQNSSVF*DLVIKYSAFDPL
ParentalLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPA-PPLDAVEQILPTLVRLLHHDDPEVLADTCWAISYL
L.LLAVPD.SSLACGYL.NLTWTLSN.C..K........A.E.ILPTLV.L.H..DPEVL.DTCW.I.Y.
RetrocopyLVLLAVPDISSLACGYLDNLTWTLSNFCSGKDHT<THVGAIEEILPTLVHL-HCSDPEVLGDTCWIITYH
ParentalTDGPNE-RIEMVVKTGVVPQL-VKLLGATELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSL-LT
T.GPNE.R.....K....P.L...L..A.EL.IVT..LRAIG.IVTGTDEQTQVVID.GA.A.FPSL...
RetrocopyTVGPNE>RLKWL*KEELCPSL>ETLERAPELLIVTSVLRAIGSIVTGTDEQTQVVIDVGAFAIFPSL<VM
ParentalNPKTNIQKEATW-TMSNITAGRQDQIQQVVNHGLVPFLVGVLSK
.PKTN.QKEA.W..M.N.T...QDQ.Q.VVN.GLVPFL.G.L.K
RetrocopyTPKTNTQKEAMW<EM*NMTSACQDQTQ*VVNQGLVPFLIGILRK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_amel_440 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_440 was not experimentally validated.

Retrocopy orthology:
Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 23 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000018411 3 retrocopies
retro_amel_1161, retro_amel_1318, retro_amel_440 ,
Bos taurus ENSBTAG000000122251 retrocopy
retro_btau_1830,
Canis familiaris ENSCAFG000000115982 retrocopies
retro_cfam_648, retro_cfam_90,
Cavia porcellus ENSCPOG000000263181 retrocopy
retro_cpor_46,
Dasypus novemcinctus ENSDNOG000000191516 retrocopies
retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus ENSECAG000000205732 retrocopies
retro_ecab_1017, retro_ecab_1123,
Echinops telfairi ENSETEG000000044452 retrocopies
retro_etel_346, retro_etel_347,
Felis catus ENSFCAG000000019362 retrocopies
retro_fcat_1176, retro_fcat_921,
Homo sapiens ENSG000001824811 retrocopy
retro_hsap_2950,
Gorilla gorilla ENSGGOG000000275352 retrocopies
retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus ENSMLUG000000279467 retrocopies
retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta ENSMMUG000000182563 retrocopies
retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica ENSMODG000000038971 retrocopy
retro_mdom_271,
Mus musculus ENSMUSG000000183621 retrocopy
retro_mmus_229,
Nomascus leucogenys ENSNLEG000000017493 retrocopies
retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Oryctolagus cuniculus ENSOCUG000000159134 retrocopies
retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii ENSOGAG000000276727 retrocopies
retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii ENSPPYG000000085691 retrocopy
retro_pabe_3501,
Pteropus vampyrus ENSPVAG000000049762 retrocopies
retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus ENSRNOG000000153291 retrocopy
retro_rnor_42,
Sarcophilus harrisii ENSSHAG000000113911 retrocopy
retro_shar_165,
Tupaia belangeri ENSTBEG0000000627414 retrocopies
retro_tbel_1635, retro_tbel_2077, retro_tbel_2672, retro_tbel_2792, retro_tbel_290, retro_tbel_3638, retro_tbel_4120, retro_tbel_4358, retro_tbel_4414, retro_tbel_4435, retro_tbel_4558, retro_tbel_810, retro_tbel_97, retro_tbel_976,
Vicugna pacos ENSVPAG000000018553 retrocopies
retro_vpac_124, retro_vpac_162, retro_vpac_163,


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